Ark of the Apocalypse
by Phoenix Nova
Summary: One full year after the destruction of Midway Station Dr. Jackson finds information on an Ancient device of great power. Carter, McKay and Sheppard are haunted with visions of a man they can't remember, and Atlantis' only hope may be no more than a myth.
1. Chapter 1: Daniel's News

Tis the season for sequels, I wanted to have Michael be the villian, but that wouldn't have worked out, any way read, review, enjoy.

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Stargate Atlantis: Ark of the Apocalypse

Chapter 1 - Daniel's News

**SGC - Carter's Lab**

Carter worked in her lab at Stargate Command.

Teal'c walked in.

"Am I interrupting?" The Jaffa asked.

"Going over some old mission report, from when I was in Command of Atlantis." Carter replied, then turned from the stack of files.

"What can I do for you?" Carter asked.

"Colonel Mitchell, and Daniel Jackson noticed you have eaten very little today." Teal'c began.

"I know, but, I've been busy, and. . ."

"And yesterday, and the day before that." Teal'c interrupted.

"I see your point." Carter said, something was obviously bothering her.

"You have not been the same since returning from Atlantis." Teal'c observed.

". . .I keep seeing flashes of a man in my mind." Carter started. "I don't know who he is."

"How long have you had these manifestations?" Teal'c asked soberly, after a brief but poignant pause.

"About three or four days." Carter replied. "Now something else is odd. These mission reports, I have no memory of filing them, or even writing them." Carter began.

Teal'c raised his eyebrow in intrigue.

"As far as I can tell, I have a memory gap of about six days, maybe seven." Carter started.

"I too, have noticed certain inconsistencies." Teal'c admitted, certain something was amiss.

"I'd better go talk to General Landry." Carter said, then walked out the door followed by the hulking Jaffa.

**Stargate Command - Briefing room**

"You wanted to see me?" General Landry asked.

Carter was hesitant to reply.

"It doesn't have anything to do with Colonel Mitchell and Dr. Jackson's recent 'concerns', does it?" General Landry asked.

"Yes, sir." Carter started, but something was wrong. Carter was awake, but unresponsive. Lights seemed to grow brighter, then the lights faded. Carter was standing on the balcony over looking Atlantis, and there were words on the winds. "There is a ship." the words echoed.

The sound of rushing water filled Carters ears, and she turned to see a whirlpool in the distance the whirlpool seemed insignificant, but Carter felt a little apprehensive.

"Hurry, you must find the ship, they won't let me hold this off much longer!" the voice called.

Soon the whirlpool expanded into a maelstrom that could effortlessly swallow the Gigantic Lantean city.

Carter's breath caught in her throat.

"Colonel Carter?" General Landry asked.

Carter snapped back to Stargate Command.

"Are you alright?" General Landry asked.

Carter was in shock.

"I was standing on the central spire of Atlantis." Carter began.

"And there was this whirlpool. It must have been at least thirty miles across, and it looked like it stretched down to the sea bed."

"That's one big whirlpool." General Landry said browsing at a file he was reading over, he seemed skeptical. But knew Carter well enough to know if she was crazy.

"I'm just estimating the distance across, Sir. It covered the length of the horizon." Carter explained.

"And Dr. Lam can't find anything wrong with you?" General Landry asked.

"No, sir." Carter replied.

Carter paused, then spoke. "Sir, this has been going on for several days."

"I read the initial reports." The General Admitted.

"The only way I'm going to understand it to go to Atlantis." Carter said, hoping Landry would grant permission to go back to her former command.

The General sat back in the chair, clasped his hands, and placed his forefingers on his chin.

"Dr. Jackson was running late. Something he found on P9X-389 lead him to believe there is information about an artifact of 'Historic Value' hidden in Atlantis' database. I've given him the green light."

General Landry thought for a second. "I want you to accompany him to Atlantis. Dr. Jackson will brief you on the way. The Apollo leaves tomorrow." then added "And while you're away, I want you to look at some plans the former Ori followers have given us, and pick a suitable site. They've offered to build a Supergate in the Pegasus galaxy."

"How did that go over?" Carter asked, pushing the thought of the giant water vortex out of her mind.

"The I.O.A. was hesitant, but the Prior said that they could equip all of the Supergates with a shield. They caved. I guess sending ships to Atlantis in a matter of hours, rather than weeks was too much for them. President Hayes gave us the green light." General Landry replied as Daniel walked in.

"Nice of you to join us, Dr, Jackson." General Landry offered.

"I'm just going to get to the point." Daniel said, he seemed more excited than he was on his first trip to Atlantis.

"I think I found it." Daniel began.

"Found what, Dr. Jackson?" General Landry started is his impatient/bored tone.

"The Ark of the Covenant."

* * *

My first thought was the Ark of Truth, but that seemed the most logical choice that everyone would choose, and I do things that nobody else does, so, yeah.

I won't reveal the true villian until very late in the story. Mwuahahahahahaha!


	2. Chapter 2: Echoes from an unknown past

I think this chapter will be very pleasing to any fan I may or may not have, I hope you like it.

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Stargate Atlantis: Ark of the Apocalypse

Chapter 2 - Echoes from an unknown past.

_**Apollo**_** Mess**

As the _Apollo _hurdled through hyper space en route to the Pegasus galaxy Carter was pouring over the data that the Prior provided only a few weeks earlier.

In the event that a suitable planet was found, and the Supergate constructed in the Pegasus galaxy, Carter knew the Odyssey would be waiting at the milky way Supergate.

The Apollo had nearly reached M35-117, the new home of Atlantis.

Carter was not present when the expedition members fled their previous planet in an attempt to escape a Replicator satellite weapon more than a year and a half earlier, but did remember having tough shoes to fill in the wake of losing Elizabeth Weir.

Daniel entered, and sat down. "So, how are things?" Daniel wanted to talk, more specifically, he wanted to talk about what was bothering his long time friend.

Carter looked up, the wear over the last three weeks of searching for a suitable planet was beginning to show.

"I've narrowed the choice down to these planets." Carter said showing her friend and colleague a tablet with three planets.

"I meant, have you . . ." Daniel searched for a word that didn't make it look like he thought she was crazy. Carter realized what Daniel was getting at.

"Not in a while." Carter admitted.

But then she thought for a moment, since the Apollo left Earth orbit, she had been hearing a word being called out. But she decided to keep it to herself.

"How long until we drop out of hyper space?" Carter asked.

"Not long, I was just here to get a bite to eat." Daniel sheepishly said, then admitted to the real reason he was there. "Also see if you were ok."

"See if I'm. . ." Carter noticed someone in the corridor pass by the entry to the mess, someone she didn't recognize, but the man did seem familiar.

Getting up she hurried into the corridor, and look for him. He was nowhere to be seen.

"Sam, are you okay?" Daniel asked.

"Did you see the crewman that just walked passed this door?" Carter asked.

"I didn't see anyone." Daniel admitted, shrugging off the claim.

Something sparked a memory, so Daniel decided to recount a story.

"After I resumed my human form, following my ascension, I remembered having vague flashes of people, places. At first I thought I was crazy, but then . . ." Daniel stopped, Carter picked up.

"The liberation of Erebus." Carter said, referring to Ba'al's naquadah mining facility, liberated several years earlier.

"I think someone is trying to tell you something - important. And they're breaking a lot of rules in doing so." Daniel said.

The voice of Colonel Ellis interrupted the tension.

"All hands prepare to drop out of hyper space."

The Apollo emerged from a hyper space window, and Atlantis' new home world hung in the weightlessness of space.

**

* * *

**

Apollo Bridge

Carter and Dr. Jackson entered the bridge as the Apollo began its final approach toward the huge city.

"We have permission to land. Commencing landing cycle." the helm announced.

"Prepare to off-load the supplies." Colonel Ellis requested. Then noticed Carter. "I assume you've selected a suitable planet for the Prior to build the Supergate?" Ellis asked.

"Not yet, but I have narrowed it down to three planets, I was going to ask Mr. Woolsey to send a few jumpers to the two that have a gate." Carter replied.

"And the one that doesn't?" Ellis asked, knowing Carter was about to request the Apollo go and investigate the third planet.

"That's where I need the Apollo. There is a gate but I need the Asgard sensors onboard the Apollo, according to our intel, the star went supernova about six hundred years ago, I want to make sure all the residual radiation has dissipated.." Carter confessed.

"Give us the coordinates, and we'll check it out after the briefing." Ellis agreed.

**

* * *

**

Atlantis Gate room

A bright flash filled a small corner of the gate room, then subsided.

"Welcome back to Atlantis Dr. Jackson, Colonel Carter, Colonel Ellis." Richard Woolsey said greeting each of the new arrivals in turn. Then directed a hand towards the briefing room. "Shall we?"

Woolsey wasted no time.

**

* * *

**

Atlantis Briefing room

"The Prior promises a shield much like the one on the Atlantis gate could be installed, and it would draw its power from the singularity." Carter said.

"What about an IDC?" Sheppard asked.

Everyone looked at Sheppard.

"Just curious." Sheppard defended.

"The Apollo, Odyssey, and Daedalus, as well as any friendly ship can have a ship S.I.D.C. A Ship Identification Code." Carter explained.

"Now as of yet, I have not selected a planet. But I have narrowed it down to these planets." Carter said.

"M3K-119, it is a rogue planet that sits outside of a demolished solar system, this planet I have asked Colonel Ellis to investigate, as it no longer has a Stargate at the moment."

Carter went on to the next planet. "M6R-042" Carter paused. "It's covered in a desert, but there are ruins not too far from the gate."

"Define 'not too far'." Rodney asked.

"It will take about an hour by jumper." Carter replied.

"Your definition of 'not too far' is not that same as mine." Rodney claimed.

"Moving on, the third planet is M1G-007, there is humanoid life, but there is not much else. Colonel Sheppards team will be going to M1G-007 and see about relocating the inhabitants to another world, Dr Jackson is going to be taking Major Lorne's team to M6R-042. I will be onboard the Apollo when they go investigate M3K-119." Carter said.

"Sounds like a plan." Colonel Sheppard said.

"Of course, you'll need my approval." Woolsey intervened.

The room fell silent, Woolsey weighed the pros and cons of loaning some of his best men, and eventually conceded.

"Gear up!"

**

* * *

**

Atlantis Main Jumper Bay - One Hour Later

With the Apollo on its way, and Sheppards team on M1G-007, it was Daniel Jackson, and Major Lorne's turn, and their destination M6R-042.

Major Lorne entered the jumper, closing the rear hatch. Then approached the pilots seat, and sat down.

"Dialing M6R-042!" Major Lorne said as he punched in the symbols.

The seven chevrons lit up and the unstable vortex exploded outward, then subsided to a glowing vertical pool of water.

As soon as the team received confirmation that the wormhole was connected, Major Lorne lowered the jumper in to the Gate room, and proceeded through the Stargate.

Emerging from the event horizon a member of Major Lorne's team noted how barren the landscape was.

"Yeah, it just goes on and on." Major Lorne agreed

**

* * *

**

**M1G-007**Sheppard and his team had only emerged from the wormhole a few minutes earlier.

Colonel Sheppard and his team were about a mile from the gate when Sheppard saw a man. He thought he recognized the man, but couldn't remember anything about him. The man was about fifteen yards away, pointing to his right.

Then they say it, a huge smoking crater.

"That's funny, there's supposed to be a village here." Sheppard said, his voice betraying a hint of concern and panic.

* * *

Thank you for reading, Chapter three will be coming soon, thanks for your reads, reviews, and comments.


	3. Chapter 3: A bit of bad news

I hope you like this chapter, I know I liked it. Thanks for reads, reviews, and what-not

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Stargate Atlantis: Ark of the Apocalypse

Chapter 3 - A bit of bad news . . .

**M6R-042 - Ancient Ruins**

Daniel Jackson had been poking around for the better part of three hours, Major Lorne and his team were getting rather bored.

"Having fun, Dr. Jackson?" Major Lorne asked.

"Yeah, why?" Daniel asked without batting an eye.

"Well, that's just great." Major Lorne sarcastically remarked.

Daniel didn't say anything.

"That was sarcasm!" Major Lorne reminded.

"Yeah, I was on SG-1 with General O'Neill for six years. I'm sort of used to it."

Daniel paused,

"Whoa, this is interesting, and yet that makes no sense."

"Have you found something?" Major Lorne asked.

"Maybe." Daniel said as he continue reading the glyphs on the wall, and then realized something.

"Most of these lines are cut off mid-sentence, sometimes in the middle of the word." Daniel explained. "There must be some kind of door here." Daniel said.

"Well, let me know if you find it." Major Lorne said as he leaned against the wall. Without warning the wall opened and Major Lorne fell backwards.

"Found it!" Daniel announced, then gathered up a few things and went inside, helping Major Lorne up on the way.

Inside there was a table control panel, much like the one on P4X-639, and the now ruined Dakara.

"Oh, great! Another puzzle. Boy am I glad we weren't sent here to scout the area." Major Lorne replied sarcastically.

"Sorry, but this used to be a place where the Ancient used to come, and they might have left something important behind." Daniel challenged.

"Something important?" Major Lorne asked.

"Yeah, though, not as important as the artifact I came to find." Daniel replied.

"And what's that? The Ark of the Covenant?" Major Lorne asked.

"Yep." Daniel replied simply.

* * *

**M3K-119 - Onboard the **_**Apollo**_

The _Apollo _drops out of hyper space.

"Begin sensor sweeps." Colonel Ellis requested.

After a minute a response came. "All I'm getting is minor planetoid, and some background radiation."

Then a small hyper space window opened. "We have a hyper space window."

"Can you identify the ship?" Colonel Ellis asked.

"It looks like a probe, only four meters across."

"It's scanning the area."

The probe began firing on the Apollo as soon as it was detected.

"Shields up!" Colonel Ellis ordered. "Fire all forward rail guns."

The Apollo let loose with all forward rail guns.

"No effect!"

"The shields cant take much more of this. It those weapons, they're over powering our shields."

"Ready the Asgard beam weapons." Colonel Ellis ordered.

"Ready."

"Fire at will!"

Several blue beams erupted from the ship and struck the probe, and it was destroyed.

"Where did that probe come from?" Colonel Ellis demanded.

Carter looked up from her screen.

"I think I may be able to answer that." Carter said.

"How?" Colonel Ellis asked.

"When to probe was destroyed it released several objects, one might be a flight data recorder." Carter replied. "Request permission to beam them aboard." Carter said as an afterthought.

Colonel Ellis just nodded in approval, and Carter made the necessary calculations and beamed three objects to the bridge.

One was a cube-shaped object, obviously the flight data recorder, the second could not be identified as of yet, but the third was the most obvious . . . a Zero Point Module.

* * *

**Atlantis Gate room - Sheppards team is returning from M1G-007**

"As far as we can tell, the entire village wasn't just leveled, it is nothing more than a smoldering crater." Sheppard said to a waiting Woolsey.

"We haven't heard from Major Lorne or Dr. Jackson. But they're not due to check in until tomorrow." Woolsey informed. "But we did hear from the Apollo, they had dropped out of hyper space, and fell under attack."

"Who was it?" Sheppard asked.

"We don't know, but their weapons were being powered by a Z.P.M." Woolsey replied.

"Oh, crap!" Rodney said.

"What?" Sheppard asked.

"The ship that attacked that village must have been using a Z.P.M., so that either means there are still some Replicators, or someone worse that knows how to build Zed PM's."

"As soon as the Apollo returns, I'll contact Earth, and request the Daedalus, and the Odyssey." Woolsey said. "I just hope that thing doesn't come looking for any other populated worlds.

* * *

**M3K-119 - Onboard the **_**Apollo**_

Carter was working in engineering when Colonel Ellis entered.

"You wanted to see me?" Colonel Ellis asked.

"Yes, I have been able to tap the Z.P.M. in to the Apollo's power grid, and it is powering the entire ship."

"But?" Colonel Ellis asked.

"The bad news." Carter paused. "The flight data recorder indicated that the probe made a stop before coming here – M1G-007." Carter divulged.

"When?" Colonel Ellis asked.

"Six hours ago." Carter replied. "And that's not the worst of it. The other device, it turns out that it's a homing beacon. Now I have been able to deactivate the beacon, but the damage has already been done." Carter said.

"I need to know everywhere the probe has been."

"Understood."

Colonel Ellis contacted the bridge. "Contact Atlantis, we're going to investigate M1G-007."

* * *

**M6R-042 - Ancient Ruins**

Daniel had been working on the table interface for two hours, before he stumbled on to the coding system.

"Ok, that make sense." Daniel said.

"What?" Major Lorne asked.

"This is like an ancient D.H.D., we just need to input the correct series of seven symbols to activate it." Daniel replied.

Major Lorne looked at the device and noticed everything was in Ancient.

"Sorry, my Ancient is a little rusty." Major Lorne said. "Wait, there aren't thirty-six panels here."

"True, but the gate address to planets like Proclarush Taonas, the name of the planet is the gate address." Daniel explained. Major Lorne just looked confused.

"Never mind." Daniel said, then tried to input the gate address to Earth.

"Ok, that's not it." Daniel said realizing he was missing most of the symbols.

"Try the gate address to Atlantis." Major Lorne suggested.

Daniel manipulated the panel, until he had the desired code input.

"Well, here goes nothing." Major Lorne said.

Daniel pressed the button.

* * *

Sheppard looked down the hallway somewhere in Atlantis.

Sheppard heard a voice.

"John Sheppard. You have to find it." The voice trailed off, Sheppard heard a word, but was unable to understand.

"Find the ship." The Voice said, filled with desperation.

Sheppard looked around to see where the voice was coming from. Then ran down the hall, following where he thought the voice was coming from.

Sheppard entered a door he thought was the mess, only to find himself on the east pier, off in the distance was a small water vortex and it was rapidly expanding.

"Hurry, time is running out." The voice was behind Sheppard, turning he found himself atop the central spire, and the maelstrom covered the entire horizon.

Sheppard's heart leapt to his throat, and he went pale.

Then the worst thing imaginable happened. . . the city began to sink in the wake of the maelstrom.

Then Sheppard woke up in a cold sweat.

"Colonel Sheppard, we're receiving a message from the _Apollo_, they'll be landing on the east pier soon." Richard Woolsey informed.

"I'll be there in a few minutes." Sheppard said.

* * *

**Atlantis - Stargate Ops**

Carter, and Colonel Ellis beamed in, and were greeted again by Sheppard and Richard Woolsey

"Welcome back, Colonels." Woolsey said.

"I'd like to go over the info we've gathered so far. We'll just have to wait on a final decision until Daniel gets back." Carter said as they climbed the stairs to the control room.

* * *

**M6R-042 - Ancient Ruins**

"That's it?" Major Lorne asked.

"That's it!" Daniel replied.

Daniel and Major Lorne stared, slack-jawed at a holographic figure. Soon the figure spoke.

"I am Tylanus, I am one of Janus' assistants. In the years leading up to the climax of our war with the Wraith. The Asgard helped us build a ship. We built this ship, and it was done unknown by the Lantean council. It was supposed to be the key in winning the war with the Wraith, but when the war went critical we were unable to get to the ship. But we knew that it would be needed one day."

The hologram faded, and an alcove opened, revealing a crystal.

Daniel picked up the crystal and found himself in a brightly lit cloud. There was a voice talking to him.

"Dr. Jackson, you must hurry back to Atlantis, and make sure that crystal makes it there!" the voice pleaded.

When the light lifted, Daniel was barely conscious, mumbling incoherently, and being carried to the jumper, the ruins collapsing around them.

* * *

I thought I'd leave you hanging, aren't I a stinker? What is the connection between the three planets? Is it really a coincidence? Chapter 4 is coming soon.


	4. Chapter 4: Hurry home, find the key

This chapter may be a little confusing, I tried to tell the story and keep it brief, I hope I did an okay job. I hope you enjoy this chapter!

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Stargate Atlantis: Ark of the Apocalypse

Chapter 4 - Hurry home, find the key!

**Atlantis - Stargate Ops**

"Incoming wormhole." Chuck announced.

Major Lorne's voice came in through the radio. "Dr. Jackson is unconscious."

"Drop the shield." Woolsey hurriedly permitted, then linked with Dr. Keller.

"Dr. Keller, medical emergency in the main jumper bay." Woolsey advised.

The shield came down. Seconds later the jumper emerged from the event horizon. And went to the jumper bay to park.

Woolsey went to the main jumper bay to get a preliminary report.

* * *

**Main Jumper Bay**

"What happened?" Woolsey asked of Major Lorne.

"He picked up this crystal, and fell unconscious." Major Lorne explained.

Dr. Keller arrived, and Daniel was loaded onto a Gurney.

"His pulse is normal. That doesn't make any sense." Jennifer said. Then turned to the nearest person. "I need to get him under a scanner!"

* * *

An unfamiliar man was standing over a very confused Daniel Jackson.

"What's going on?" Daniel asked. "The last thing I remember I picked up a crystal on M6R-042."

The figure said nothing, just turned to reveal the wall of a temple.

Daniel was perplexed. He recognized it. It was King Solomon's temple, in Jerusalem.

Night had fallen, and several people dressed in ceremonial attire, obviously Priests, were entering the temple.

There was a thick blanket of tension in the air.

Following them Daniel saw something. The familiar box-like shape with two winged figures atop the golden coffer – The Ark of the Covenant.

"I don't get it." Daniel said, hoping to draw a comment from the figure, but to no avail.

The priests were moving it.

Daniel turned back to the figure only to see he was no longer in the temple, but in a network of tunnels, and the Ark was being moved past him.

Daniel and the priests rounded a corner and found themselves outside.

Daniel spotted the figure again, and realized they were somewhere else all together.

"Mt. Sinai!" Daniel said. Then followed the four man procession with the strange figure right behind.

Daniel followed the priests into a cave, and soon came to an area where the tunnel turned downward. Eventually coming to a series of pillars.

Then everything went dark.

"Dr. Jackson, you need to find the Ark, only you know how to find it. It's the key to the ship." the figure said.

Something he said to Carter a few days earlier came to mind, and he realized who, or rather what he was talking to.

"Do you realize how many rules you're breaking?" Daniel asked.

"A lot, but enough of us know what's at stake. I've done all I can." the man said.

"Yeah, I've heard that before." Daniel challenged.

The face on the man seemed maddeningly familiar.

"Do I know you?" Daniel asked.

"Yes, we met briefly." the man said, then looked behind himself. The man then turned to light with tendrils, and floated away.

* * *

**Atlantis - Infirmary**

Daniel woke up to see Colonel Sheppard talking with Carter and Woolsey.

Then they realized Daniel was awake.

"Morning, sunshine." Sheppard said.

"Morning? How long was I out?"Daniel asked.

"Four days." Jennifer Keller replied.

"Four days?" Daniel asked.

Carter interrupted, mostly to divert Daniel from the strange ordeal.

"I thought you'd like to know, we've selected a target for the Supergate. The Apollo should be here within the hour with an unused gate from the gate bridge. The Supergate will be up and running in the next seventy-two hours." Carter said.

"Great, which planet are we compressing to a singularity?" Daniel asked.

"M3K-119." Carter replied.

* * *

**Three days later - Holo Room**

Daniel spent the brunt of the last three days researching the Ark of the Covenant. Possible location, history.

Sheppard walked in.

"Hey, Dr. Jackson. The Apollo is about to leave, did you want to watch this?" Sheppard asked.

Suddenly Daniel got really excited. "It's on Earth." Daniel said excitedly.

"What's on Earth?" Sheppard asked.

"The Ark of the Covenant." Daniel replied.

Daniel gathered a few things, and walked out the door. A couple seconds later, Daniel walked back in.

"Are you coming?" Daniel asked. "I have to get back to Earth, as soon as possible." Daniel said.

A call came in over the radio.

"Colonel Sheppard, the Prior is here." chuck announced.

"On my way." Sheppard replied.

Sheppard and Daniel went to the nearest transporter, and made their way to Stargate Ops.

* * *

**Atlantis - Stargate Ops**

Sheppard and Daniel arrived at Stargate Ops to see a pale skinned man with milky white eyes, holding a staff with a blue crystal.

"I bring greetings from Tomin, our leader." The Prior announced.

They exchanged greetings, then Woolsey suggested they prepare to leave.

* * *

**M3K-119 - Planetary Orbit**

The Apollo dropped out of hyper space in the ruined star system.

"So, what now?" Daniel asked.

"Beam the gate, myself, and Dr. McKay down to the surface." the Prior instructed.

Colonel Ellis nodded.

A bright flash filled the bridge, then faded marking the Prior's departure with Rodney McKay.

After a moment Rodney's voice filled the speakers.

"We've started to compress this planetoid. I'll keep you posted as progress is made." McKay said.

"Understood, Apollo out." Colonel Ellis said.

"I'm going to monitor their progress from Engineering." Carter said, then excused herself.

* * *

**Apollo - Bridge**

The crew of the Apollo had been watching a blue bubble form and expand for the better part of twelve hours. It had nearly covered one-tenth of the planet before Rodney called.

"The Prior said to open up with out Asgard weapons."

"Are you crazy, Dr. McKay?" Colonel Ellis asked.

"The force field, which you should be able to see from orbit will provide more than sufficient protection from the weapons fire." The Prior assured.

Colonel Ellis gave the order.

"Target the center of the force field, and fire at will."

The Apollo began to unleash the full brunt of her Asgard weapons. Within an hour the field had increased in size, and was covering more than three quarters of the planet.

"Good, another minute or two, and the planet will be completely encompassed by the force field." Rodney announced. "Then the fun part begins."

* * *

**M3K-119 - Planet Surface**

The Prior finished establishing the force field over the entire planet.

"I have begun to collapse the planet. We will need to evacuate quickly." the Prior warned.

"Understood." Rodney said then activated the link on his headset.

"We're ready for extraction." McKay said.

McKay and the Prior vanished in a flash of light.

* * *

**Apollo - Bridge.**

"Welcome back, Dr. McKay." Colonel Ellis greeted as Rodney arrived.

"Yes, yes. Thank you." McKay said as he made his way to a station where he could monitor the collapse of the planet.

Several dozen of the segments that make up the Supergate were already in position, and more were emerging from the shrinking planet.

"The planets overall mass has been reduced by fifteen percent." McKay announced. "Supergate structure is at eleven percent."

* * *

**Atlantis - Mess**

A Call came into Richard Woolsey's headset, in the middle of a conversation he wanted to get out of.

"Mr. Woolsey, we have an unscheduled off-world activation. It's Ladon Redim." Chuck reported.

"I'm on my way." Woolsey said.

* * *

**Atlantis - Control room.**

"I have Ladon Redim, for you." Chuck said.

"This is Richard Woolsey."

"This is Ladon Redim of the Genii, I have information that the Wraith are almost ready to launch an assault on Atlantis."

Woolsey looked at Chuck, not sure whether or not to trust the word of Ladon Redim.

"For the last eight months there has been some unusual storms over the planet preventing them from leaving, but the storms have completely subsided." Ladon Redim admitted.

"Give us coordinates, and we'll go investigate." Woolsey compromised.

"I don't think you understand. They're on the way right now. More than a thousand Hive ships. Each is flanked by between three and four cruisers." Ladon said. "They'll be there in four days."

* * *

Well, that's that, a huge fleet. And just so there's no confusion the Ark is required to use the ship Carter, Sheppard and Daniel Jackson are being told about. More info will be released in regard to the Ark of the Covenant in future chapters

Thanks for the reviews. Theories? Ideas? Things you'd like to see?


	5. Chapter 5: A Voice From the Dust

This is when things get REALLY interesting, and a little confusing, but it will all be explained by the end of the story, I promise.

* * *

Stargate Atlantis: Ark of the Apocalypse

**Chapter 5 - A voice from the dust . . .**

Pegasus Supergate - Onboard the Apollo bridge.

"Colonel Ellis, we've got a communication from Atlantis."

"Let's hear it. Colonel Ellis directed. .

It took a second to patch the

"Colonel Ellis, we've recently received intel on a Wraith fleet that has been amassing." Woolsey familiarized.

"Give us the coordinates, we'll go check it out." Ellis suggested.

"We've already sent a team to a nearby gate to check things out. There are more than a thousand Wraith Hive ships headed for Atlantis. We have Four days until they arrive."

Colonel Ellis turned to McKay, who had the 'I want to go help so I can be the hero' look. Then directed his next comment through the comms to Woolsey.

"We'll drop McKay off, and the Odyssey will return Dr. Jackson to Earth and inform Stargate Command of the situation." Ellis said.

"Understood." Woolsey confirmed.

"Good luck."

* * *

**Janus' Super Secret Lab**

Carter had spent most of the last few days going over anything in the labs she and Zelenka could get their hands on.

"I don't get it, what are we looking for?" Radek asked.

"I'm not sure." Carter realized Zelenka was about to call it quits.

"According to the hologram Daniel saw, the Asgard helped Janus build a ship, and if it's the one I keep hearing about in these . . ." Carter was cut off.

"Visions that an Ascended Ancient was showing you?" Zelenka asked.

"Have you been talking to Daniel?" Carter asked.

"I stopped by the holo room while he was looking for the Ark." Zelenka admitted.

Carter's expression changed, and suddenly she was on the eastern pier, the odd thing is. There was only one moon out, when there should have been three.

There was a violent and abrupt disruption of the water half mile away from the city, and a maelstrom formed, and very quickly expanded.

The edge was encompassing most of the eastern pier, then the wind carried a word passed Carters ears

"Leviathan!"

The word was repeated as the volume faded, almost like an echo.

Then a massive ship emerged from the depths of the sea, throwing water everywhere.

The ship rose, and began to hover over the city.

"Colonel Carter."

Carter's attention was pulled down to see a man that seemed familiar, but she couldn't remember him.

"This ship, the Leviathan, was going to be the ship that saved Atlantis from the Wraith ten thousand years ago. But the Wraith attack came on so suddenly, they couldn't take the chance going for it. So they took the key to it's operation back to Earth, and left the ship." The man said.

"Aren't you breaking a lot of rules even allowing me to see you?" Carter asked.

"I've managed to distract the rest of the Ascended beings. But time is running out."

"Where is the ship?" Carter asked.

"Sometimes, you have to go back to where you began." the man cryptically replied.

"What about the key?" Carter asked.

"Daniel went back for it." the man replied.

"You're being awfully cooperative for an ascended being." Carter pointed out.

"Allow me to explain why. About a year ago, Atlantis was under attack when Rodney left an Ancient warship in orbit."

As the man explained who he was, the memories flooded back.

"Soon you won't remember any of this. Soon all you will remember will either be a Wraith onslaught where everyone is dying, or a decisive victory where you gain another, massively powerful ship."

"Colonel Carter?" Zelenka asked.

Carter turned to the voice of Zelenka, and realized that the Ascended being was gone.

But rather than look for him, Carter's focus went into overdrive.

"Search for the name 'Leviathan' in Janus's records." Carter asked.

* * *

**Atlantis - Stargate Ops.**

Dr. McKay appeared in a flash of white light.

"Dr. McKay, how did the Supergate test go?" Woolsey asked.

"We're about to be overrun by Hive ships, and you're worried about the Pegasus Supergate?" McKay asked.

"I asked, because, then we can possibly get reinforcements from three galaxies, instead of just this one." Woolsey corrected. "I've already contacted the coalition, they're assembling a committee to gather ships and resources." Woolsey added.

"Ellis is taking Dr. Jackson to meet up with the Odyssey, he's heading back to Earth to find the Ark of the Covenant. And in the meantime he's going to see about rounding up some more help, maybe this defeat won't be too bad." McKay ensured. Then did a double take.

"I didn't realize the coalition had the resources we need." Rodney pointed out.

"They don't, but every little bit helps." Woolsey replied.

"Any emphasis on the word 'little'?" Rodney asked.

"Getting back to the threat at hand, where are you going?" Woolsey asked.

"Well, I was going to look at the Zed P.M. the Apollo got from the attack drone." McKay said hoisting a case, containing the Z.P.M. "Maybe we can get some more power for the Drone platform and the shield.

McKay excused himself.

* * *

**Apollo - Milky way Supergate.**

The Apollo had crossed through the Supergate and made the hand off of Dr. Jackson to the Odyssey.

With the hand off made, the Odyssey headed for Earth.

The Apollo headed off to find help in defending Atlantis.

* * *

**Odyssey - Bridge.**

"Welcome to the Odyssey, Dr. Jackson." the Commander, Colonel Cameron Mitchell greeted.

"Mitchell, you get the transmission?" Daniel asked.

"Sure did." Colonel Mitchell replied, then turned to his pilot.

"Set a course for Earth, and engage the hyper drive." Colonel Mitchell said.

Colonel Mitchell leaned over to Daniel.

"I always thought it was in a military warehouse in Nevada."

The ship jumped to hyper space.

* * *

**Janus' Super Secret Lab**

It was almost two hours, before any sort of results appeared on the screen, Zelenka was about to give up.

But then something happened.

"This is interesting." Carter said.

Zelenka looked, not expecting to see anything of any significance.

"What is it?" Zelenka asked.

"It's an encrypted directive." Carter replied.

"Can you decrypt it?" Zelenka asked.

"I don't know." Carter replied going to work.

But it wasn't long before Carter stumbled onto an algorithm that seemed to be working, but the directive still seemed to be locked, but Carter was able to gain enough access to know what it did.

"This directive is linked to a small compartment somewhere in this lab." Carter said still working on unlocking the directive.

Finally, she had it, and a small pedestal extended upward from the floor in the center of the room.

On it was a small device like the life-signs detector, except it was different, instead it had several buttons on the face of the device, and the screen displayed a single blip with a ring expanding outward from the blip.

Instantly Carter knew what it was.

"It must be sending some kind of signal from a homing beacon, we should be able to trace this to the Leviathan." Carter said, then grabbed a tablet, and began interfacing the tablet with the device.

* * *

**Atlantis - Woolsey's Office**

Carter walked in after a brief greeting from Woolsey.

"What have you found?" The bean-counting administrator asked.

"I think we found the Leviathan." Carter began.

There was a momentary flicker in the lights.

Woolsey activated the link on his headset.

"What's going on?"

"Mr. Woolsey, you might want to see this." Chuck said.

Woolsey stood, and looked out through the glass to see a hologram appear directly in front of the Stargate.

"I AM ANUBIS! Humans of Atlantis, your end of days is at hand. Bow before your God, and you will be spared."

"He always did have a flare for the dramatic." Carter said realizing the gravity of the situation.

* * *

The face of the true villain is revealed. Now that I think about it, this is starting to look alot like "The Lost City" from Season 7, but I promise it will not end in a similar manner.


	6. Chapter 6: A Needle in a haystack

I hope you like thie Chapter, I like the part with Daniel fumbling though the tunnels, it was kind oflike me, blindly writing anyting that looked good.

If I owned SGA I would have this made into a movie.

By the way, keep your eyes peeled for a Sea Quest DSV refence, I actually thought it was mildly amusing. But you may think otherwise.

Any way, read, review, worship if yo so desire.

* * *

Stargate Atlantis: Ark of the Apocalypse

CH 6 - A needle in a haystack

**Atlantis - Conference room.**

"I wouldn't even begin to know where to start looking." Carter confessed.

"What did you learn from the Holo-room?" Woolsey asked.

"Not much, the only Intel we do have came from an ascended being that broke a lot of rules." Carter explained.

"And all he told you meant nothing." Sheppard clarified.

"From what Daniel said 'the Leviathan was a mythical sea monster that guarded Atlantis.' But that doesn't tell us much." Carter explained.

Sheppard was still griping about the Intel from the ascended being.

"'You have to go back to where you began?' Sounds like he's not being helpful, but he wants us running around in circle." Sheppard concluded.

"That's it!" Carter declared. Everyone turned and looked at Carter, expecting a big flashy explanation.

"What's it?" Sheppard asked.

"Ten thousand years ago, Atlantis was on another planet all together. And that is the planet where the Ancients fled to Earth from." Carter explained. Nobody understood.

"Lantea!" Carter said. "The Leviathan is on Lantea."

"What about that cool device yo found in Janus' lab?" Sheppard asked.

"It must be a way of homing in on the ship." Carter guessed, her guesses were usually right.

"Requesting permission. . ." Sheppard never finished his sentence.

"Granted!" Woolsey said, knowing Sheppard could find the ship save the city.

* * *

**Earth - Stargate Command**

"Now, as far as I can tell, the Ark of the Covenant is a key to operating the Leviathan." Daniel said, managing to cut down his usual long-winded explanation.

"And you know where it is?" General Landry asked.

"Not exactly." Daniel admitted. "But my information points to it being hidden deep inside a cave in Mt. Sinai."

"What am I going to tell the Egyptian government.?" General Landry asked. "If we tell them that the Ark of the Covenant has been in their borders for the last few thousand years, they're going to demand full possession of it."

"All I know is, if we don't acquire it, then the entire Atlantis expedition will be forced to give up the city of the Ancients, or worse, they all die." Daniel urged.

"What do you propose?" General Landry requested.

* * *

**Atlantis - Gate room.**

Larrin emerged from an active wormhole.

"Sheppard, you always seem to need my help." Larrin smirked.

"You heard about the Wraith fleet that's on it's way?" Sheppard asked as the gate shut off.

"We caught wind of the Intel the Genii had obtained." Larrin admitted.

"When they finish with us, they'll likely turn their attention to the rest of the galaxy." Sheppard warned.

Larrin was losing patience.

"Get to the point, Sheppard." Larrin begged.

"We need ships." Sheppard admitted.

"Again?" Larrin boastfully inquired.

"Again." Sheppard replied

"To help defend Atlantis?" Larrin guessed, to which Sheppard nodded.

"You do know that all of our ships can't defend against a Wraith incursion of this magnitude." Larrin reminded Sheppard.

"We know." Sheppard replied. "That's why we're going for a little help." Sheppard cryptically explained.

"How are you getting there? You can't spare a ship capable of hyperspace travel." Larrin pointed out.

"True but thanks to the Replicators that we destroyed, there is a gate in orbit over the planet." Sheppard informed.

"What do you say? We fight side by side one more time." Sheppard asked.

"Fine, I'll contact some of our colonies, and see what I can come up with." Larrin agreed

"In the meantime, I'm going on a little trip." Sheppard said.

Woolsey was standing clear, he had heard some stories about Larrin, and wanted to keep a safe distance away.

As Sheppard walked away from Larrin, and towards Woolsey, Sheppard gave Chuck the go ahead to dial the gate.

"Now that we've taken care of that, I'm going up to the jumper bay." Sheppard said walking away. Then came back. "Oh, would you mind if I took Zelenka?"

Woolsey pulled a face that seemed to say 'You want McKay AND Zelenka?'

"If we do find the ship, we'll need them both." Sheppard rationalized.

"Fine."

Sheppard left to meet his team in the jumper bay.

* * *

**Earth - Stargate Command**

"It's just as we thought." General Landry announced.

"They want to take full possession of the Ark?" Daniel asked.

"Yeah. But the good news is we've managed to get permission to borrow it for 'scientific study'." General Landry announced.

"And?" Daniel asked know full well there was a 'but'.

"They want one of their people to be there when the Ark is located. Heck, I wouldn't mind being there." General Landry admitted. "But I've got my hands full right now."

"The Odyssey will beam you over there when you're ready."

Daniel nodded.

* * *

**Planetary Orbit - Lantea**

The gate that once acted as a weapon over Lantea activated, and a puddle jumper emerged from the event horizon.

The orbit had decayed in the last two years, but it was still somewhat stable.

"According to this, the ship is submerged." Carter said.

"I guess we're all going for a swim." Sheppard said as he brought the ship into the atmosphere, and soon the jumper was skimming the crystal blue water.

Carter was watching the device she found in Janus' lab, while McKay was trying to look over Carter's shoulder.

"I don't believe this. I'm still not getting a clear reading." Carter mourned.

Out of nowhere a Flagisalis leapt from the water right in the path of the jumper. Sheppard was forced to submerge the ship and accelerate to avoid hitting the giant fish.

A few seconds after the jumper was submerged by the ocean Carter made an intriguing revelation.

"That's odd. The signal just cleared up." Carter revealed.

"So where do we go, Wolenczak?" Sheppard asked.

Carter ignored the comment, then pointed.

"There!"

It was almost completely blended into the seabed except for a group of Flagisalis that were swimming around it.

"That's real nice of them, pointing the way." Sheppard said.

It took a few minutes to reach the docking bay, and board the ship.

McKay found a terminal and interfaced his tablet, while Ronon and Teyla were deployed to secure the area.

"I don't believe it." McKay began.

"What's wrong, McKay?" Carter asked.

"Wrong? Nothing, I wish we had this ship when the Replicator satellite attacked. Or during the Siege of Atlantis. I mean this ship alone could have taken on the entire Replicator fleet." At this point McKay was excitedly rambling.

"McKay!" Everyone said all at once.

"Sorry, this ship is amazing. I'm reading eight drone platforms, the shield generators are more powerful than anything that Atlantis' shields. It looks like they meshed Asgard shields with Ancient shields." Rodney was almost salivating. "On top of all that, I'm reading ten Asgard beam weapon emitters."

Carter took the tablet from Rodney and looked over the data.

"From the looks of things there the internal power grid was designed to operate on multiple Z.P.M.'s" Carter observed.

"Multiple? How many?" Sheppard asked.

"I won't know until we get to the bridge." Carter replied.

* * *

**Earth - Tunnel inside Mt. Sinai**

Daniel Jackson and an Egyptian guide had spent the last few hours poking though the deep tunnels beneath Mt. Sinai.

As they rounded a corner the guide spoke up.

"You never answered my question, why do you seek the Ark of the Covenant?" the guide inquired.

"Well, that's kind of a long story." Daniel replied.

"We have plenty of time." the guide prodded.

"The story is also classified." Daniel defended.

"So, you could tell me, but then you'd have to kill me?" the guide asked.

"Something like that." Daniel replied.

There was a pause.

"Okay, but it had better be worth it." the guide joked.

Rounding another corner, they found a dead end. But there was something odd about it. There seemed to be some odd rock mixed in with everything else, it almost looked like a symbol. Not just any symbol, it looked Ancient.

"That looks like writing." Daniel said.

The guide was confused. "Are you sure?" He had never seen such a language.

"Yes." Daniel confirmed.

"Where?" the guide asked, then stopped himself. "Let me guess 'classified'?"

Daniel touched the symbol, and the entire wall flickered and vanished.

The guide muttered something in his native tongue, his voice betrayed a hint of superstitious fear.

Daniel convinced the guide to follow him a little further, and soon the tunnel opened up to a vast cavern that housed an ancient city, hidden by time and Earth.

The cavern was exactly how he remembered it from the vision from the Ascended being.

Oddly a faint glimmer of light was coming from the ceiling of the cavern.

"What's causing that light?" Daniel asked, knowing that he was in fact several hundred feet from the surface.

He and the guide looked towards the source of the light and found there were no fissures leading to the surface. But there was a floating object in the middle of the cavern floating high above the ground.

It was a glowing sphere, which was connected to the ground by a pillar of light, at the base of the pillar of light was a building with a pillared building.

"I'm going to go check it out." Daniel said approaching the building.

Inside the building was bare except for the pillar of light extending through the ceiling in landing on the floor. The light seemed to be pointing towards something.

"There it is." Daniel said.

The guide made a reference to one or more deity. "The Ark of the Covenant." The guide finally said in awe.

The pair made their way to the Ark. Daniel took several steps forward, and began to examine the Ark.

The guide said nothing at first.

After several seconds a tense sound echoed off of the walls, a gun click.

"Step away from the Ark, Dr. Jackson." the guide threatened, obviously he was not a guide.

"Let me guess, you're a mercenary, posing as a guide that brought a gun?" Daniel surmised.

"This is going straight back to my people." the guide said.

"That's going to be a bit of a problem." Daniel admitted.

"Why's that?" the guide asked.

"Just call it a hunch." Daniel said as he and the Ark were beamed away.

* * *

**Odyssey - Bridge**

A bright light of the Asgard beaming technology grew from nowhere and subsided with Daniel and the Ark in the midst of where the bright light had appeared.

Mitchell stood, with his arms crossed. "You have it I see." The Colonel said.

"No, this is a souvenir I got from Marakesh." Daniel joked, as some crew members came forward to take the Ark to an onboard lab. Daniel was adamant that they not touch the Ark itself.

Daniel stuck around and told Mitchell about what happened, then caught up to the Ark.

"Inform Stargate Command of our status. Then set a course for the Supergate, and let's be on our way." Mitchell ordered.

* * *

**Leviathan - Bridge**

Carter, Sheppard, and McKay arrived on the bridge.

McKay and Carter sat down at key stations meant for monitoring internal systems.

"From the looks of this, the ship's main systems each ran of their own Z.P.M." Carter observed.

"She's right, Weapons, shields. But it looks like the drone platforms were tied to a different Z.P.M. than the Asgard beam weapons." McKay noted.

"I didn't notice this." Carter began.

"What?" Sheppard asked.

"It looks like the shields ran off of six Z.P.M.'s" Carter said.

"How is that possible?" Sheppard asked.

"Well, from the schematic, this ship is several times larger than Atlantis. It would require a lot more power to operate than the city. And all the extra weapons would drain a lot of power in addition to the shields." Carter surmised.

"Colonel Sheppard, please come in." Teyla requested over the radio.

"Go ahead." Sheppard said.

"We are in a weapons bay of some sort, you may want to come down here." Teyla requested.

"On my way." Sheppard said then looked at Carter and McKay. "Will you be okay if I left alone?" Sheppard asked.

"We'll be fine." McKay spiritedly replied.

Sheppard left the bridge, and found a nearby transporter.

Soon arriving at Teyla's location he found a vast room with hundreds of shelves lines with drones. The aisles were numerous, and seemed to go on for hundreds of meters. Sheppard contacted Rodney.

"Rodney, Teyla found a room full of drones." Sheppard said.

Rodney had been tracking him, and made an intriguing conclusion.

"The interesting thing is, that's not the only room full of drones there is. According to the log, there are at least fifteen other rooms like the one you're in." McKay paused. "Sheppard, there's another room, not far from where you are now. I'm getting some interesting readings." McKay asked, hoping Sheppard would check out the room.

"Define 'interesting', Rodney." Sheppard demanded.

"According to my readings it's perfectly safe." Rodney replied.

"Ok, but if I turn into a bug again, I'm coming for you." Sheppard threatened.

Following Rodney's directions, Sheppard and Teyla arrived at a room much like the room full of drones, except for one crucial detain. Instead of drones, Sheppard found Zero Point Modules.

* * *

**Supergate - Pegasus galaxy**

The Supergate activates, and two Daedalus class battle cruisers emerged from the event horizon

The Odyssey, and the Daedalus. Waiting for them is three Wraith Hive ships, oddly the Hives do not open fire.

"Colonel Caldwell, the lead hive ship is hailing us." Major Marks announced.

"Let's see it." Caldwell permitted, only to see Todd's face on the screen.

"Have you been informed as to the situation?" Todd asked.

"We have." Caldwell replied, expecting a lengthy conversation, about this and that. Maybe something about mistrust.

"We need to hurry to Atlantis, time is of the essence." Todd succinctly said, then closed the channel.

"What now, sir?" Major Marks asked.

"Signal the Odyssey to get to Lantea, and set course for Atlantis." Caldwell said.

* * *

There you go, help is on the way, and not too soon. As far a a question I was asked. Yes, the prior will render some aid in the battle, not the aid you are probably think of, but help is help I suppose.


	7. Chapter 7: The Calm of Battle

Now that they have the Leviathan and the Ark of the Covenant in the same place, maybe the playing field will be leveled, or maybe one of the two armies will also be leveled.

* * *

Stargate Atlantis: Ark of the Apocalypse

**CH 7 - The Calm of Battle**

The Daedalus dropped out of hyper space.

Assuming orbit over M35-117 Colonel Caldwell noticed a small fleet over the planet as well, then remembered a message he had received.

"Contact Atlantis, and get clearance to beam." Caldwell said.

* * *

**Atlantis Gate room.**

The gate room filled with a solar white light as Colonel Caldwell beamed in. He was met by Richard Woolsey.

"Colonel, I thought you'd like to know. Colonel Carter and Colonel Sheppard found the ship." Woolsey said.

"I hope that ship is what Colonel Carter claims it is." Caldwell contended.

"You too?" Woolsey asked, his rhetorical question seemed to foretell the dire situation of the upcoming battle.

"I just came down to tell you know that the _Odyssey_ is dropping off Dr. Jackson." Caldwell informed.

"You could have told me that over the radio." Woolsey stated, he knew Caldwell had another reason for coming all that way.

"The truth is. The _Apollo_." Caldwell began.

"What about it?" Woolsey asked curiously.

"They went to the Ori home galaxy."

* * *

_**Odyssey**_

Daniel sat in a shipboard lab, examining the Ark of the Covenant. Colonel Mitchell walked in.

"Dr. Jackson, thought you'd like to know, we're almost there." Mitchell said.

"I'm almost done here." Daniel replied.

"So, how does it work?" Mitchell asked.

"Well inside is said to be the original stone tablets containing the Ten Commandment, and the Rod of Aaron." Daniel began. "Now, it was believed that any righteous army that bore this at its head, would be invincible."

That didn't answer his question, so he deflected.

"Well that's great. We'll beam you down once we have the coordinates." Mitchell said.

* * *

**Lantea**

The _Odyssey_ dropped out of hyper space, and assumes orbit.

"I'm picking up Colonel Carters beacon." One of the crew announced.

"Are you ready Jackson." Mitchell asked over an open comm link.

Daniel was standing ready next to the Ark of the Covenant, and in a flash of light he was gone.

"Plot a course for Atlantis. Engage the hyper drive when ready." Mitchell said.

"Aye, sir."

The _Odyssey_ zipped away into hyper space.

* * *

**Leviathan - Bridge**

Daniel Jackson appeared in a flash of light.

Sheppard noticed the Ark next to Daniel.

"Is that the Ark of the Covenant?" Sheppard asked.

"No, he won the door prize!" McKay snapped.

Sheppard awkwardly moved toward the Ark, fearing he would touch it and be killed.

"Near as I can tell, the Ark is a piece of Ancient Technology, and would respond to the A.T.A. gene." Daniel explained.

Comforted Sheppard knelt down to open the Ark, then stopped and looked up.

"Are you sure?" Sheppard asked.

"Just open it!" McKay pleaded, then reached down to do what Sheppard feared doing.

"Rodney!" Carter fearfully shouted as Rodney's hand touched the Ark.

When nothing happened everybody breathed a sigh of relief.

"Are you crazy, you could have been killed." Carter chided.

"I could have, yes." McKay admitted.

"But the thought of wasting this opportunity for honor and glory, was too much for McKay." Sheppard teased.

With the Ark of the Covenant open Daniel reached in and pulled out a crystalline staff about 4 feet long.

"I wonder where that goes." Sheppard curiously said.

"There was a cylindrical recess that would fit this." Rodney said.

"Where?" Daniel demanded.

"On the bridge." Rodney responded.

* * *

**Atlantis - Stargate Ops**

"Mr. Woolsey, the Odyssey just dropped out of hyper space." Chuck announced.

"Excellent timing." Richard said in a sigh of relief.

"Major Lorne, is the weapons platform ready?" Woolsey asked over an open channel.

"For what good it'll do." Major Lorne replied, awaiting the order to fire from his seat in the control chair.

Chuck interrupted in a voice of panic.

"Mr. Woolsey, I'm detecting several hyper space windows opening."

Chuck looked up at Woolsey. "It's the Wraith fleet." Chuck sounded confused.

"What's wrong?" Woolsey asked.

"I only detect fifty ships. Most of which are Wraith, but there is a Goa'uld Command ship." Chuck explained.

"Anubis is probably holding back his main force until he can deliver his ultimatum. It's what he did six years ago when he attacked Earth." Woolsey concluded. "Tell Colonel Mitchell and Colonel Caldwell not to attack unless fired on."

A figure appeared in the gate room as chuck finished sending the order.

"Inhabitants of Atlantis, the knowledge, and technology of the Ancients will be mine, surrender, and you will serve me. Resist, and your deaths will be most excruciating." Anubis threatened.

Chuck turned to Woolsey, a thought on his mind. Woolsey seemed to read Chuck's mind, and approached the hologram. Woolsey knew he had to buy Sheppard and his team a little time.

According to the Odyssey's report, they had already found the ship, and the key to it's operation, and they had McKay and Carter working to solve the problem. He didn't have to buy much time.

"Anubis, it's been a long time." Woolsey began.

"Are you here to surrender?" Anubis demanded.

"I have a few questions first. According to our reports, you were trapped battling the Ascended Oma Desala. Obviously you escaped. What happened?" Woolsey asked.

Anubis thought for a long moment, then submitted to his ego-narcissism.

"Three years ago, when your people attacked to Ori, Oma Desala was momentarily distracted. I used that opportunity to escape." Anubis arrogantly confessed.

It seemed odd that a Goa'uld was sharing this information so blithely.

"And how is it you managed to build such a fleet in such a short amount of time?" Woolsey asked. "That would have taken thousands of years."

Anubis just chuckled devilishly.

Then it hit him.

"You have an Asgard time dilation device." Woolsey concluded.

Anubis began to laugh maniacally.

* * *

**Leviathan Bridge**

Daniel Jackson inserted the crystalline staff into the recess.

Nothing happened.

"Ok, not what I was expecting." Daniel said.

Rodney noticed something wrong. There were markings on two parts of the recess. So Rodney reached out and grabbed the staff.

"What are you doing?" Sheppard asked as Ronon, Teyla, and Zelenka walked in the door.

"Turning the key in the ignition." Rodney said, then turned the staff. The ship seemed to come alive.

"What is going on?" Teyla asked.

"Rodney got lucky!" Sheppard replied.

"What, again?" Radek asked.

Rodney glared at the Czech scientist.

"Atlantis needs our help!" Sheppard said, manning the control chair positioned in the middle of the bridge.

* * *

**Lantea - Ocean surface**

The ocean surface was calm and pristine, yet the dark water was unnerving and murky.

The surface began to get choppy and violent, until it began to churn, and swirl into a giant whirlpool as the giant ship fleet rose from the depths of its watery shrine.

Onboard Sheppard was reclined in the control chair, he seemed to be focusing on something, then a hyper space window opened up, and the ship was off.

* * *

**Atlantis - Stargate Ops**

Woolsey was interrupted in the middle of another in a long series of questions.

"ENOUGH!" Anubis shouted. "You are stalling. Surrender and serve me, or fight and die."

Woolsey turned stern. For many years his unwavering words would be remembered.

"Like Abydos? You didn't keep your word then." Woolsey reminded the half-ascended being. "If you fight, then it is you who will lose. Like every other time."

"Mr. Woolsey, I'm detecting hundreds of hyper space windows forming." Chuck said.

Woolsey turned to Chuck. "Contact the fleet, launch all jumpers. Fire at will."

* * *

**Orbit over Atlantis**

Two Daedalus class battle cruisers, two dozen traveler ships, and four Wraith Hive ships began to open fire.

From the surface Atlantis began to fire massive amounts of drones. All the while all puddle jumpers and F-302's were launched.

* * *

**Atlantis - Stargate Ops**

"How are we going to survive this?" Chuck asked.

"I don't know." Woolsey admitted.

"We've got gliders and Darts inbound." Chuck announced

Then a subtle beep that would otherwise barely be noticed seemed to stand out.

"Forty-two more ships just dropped out of hyper space." Chuck warned.

* * *

Any guesses who the 42 other ships are? Do we care? Or am I just a loony old-ish man? Sacred White Phoenix, don't say it! J/K


	8. Chapter 8: Hope on the Horizon?

Thank you for all of your reviews, I don't own SGA but **IF** I did Stargate Atlantis, this one (With some minor tweeks) would be one of the next SGA movies. You may feel differently, but here's the final chapter to Ark of the Apocalypse, read review and/or enjoy.

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Stargate Atlantis: Ark of the Apocalypse

**CH 8 - Hope on the Horizon?**

A look of dread appeared on Woolsey's face at the thought of more targets when they were already immeasurably outnumbered.

"It's the Apollo! They're contacting us!" Chuck announced.

"Let's hear it!" Woolsey enthusiastically said, hoping for some good news.

Chuck patched the incoming transmission through the speakers in Stargate Ops.

"I hope we're not interrupting!" Colonel Ellis said.

"The more the merrier." Woolsey replied.

"Good, because the Prior got forty-two Ori mother ships to join the fight."

"Ori Mother ships?" Woolsey asked.

"You heard me. They'll create a defense perimeter, and we'll do what we can." Ellis promised. "Wish us luck, Apollo out."

Just as Ellis promised the forty-two Ori ships created a defensive perimeter blocking most of the Wraith weapons fire, but even then, it was taking it's toll.

**Leviathan - Hyper space**

Rodney walked in, he had a worried look . . . more worried than normal.

"What is the matter Dr. McKay?" Teyla asked.

"Sensors detected a massive fleet over Atlantis." Rodney reported.

Teyla looked at Carter.

"How long until we are in range to fire?" Teyla asked.

"Ten minutes." Carter replied looking at the sensor readout. "But by then it may be too late."

"Ten minutes, do they even have that long?" Rodney asked.

Teyla looked at Sheppard. He read her mind.

"I'm trying." Sheppard announced.

**Atlantis - Orbit**

The fight was going better than could be expected, but still it was a fight that the Atlantis expedition was losing.

There was a single Goa'uld capital ship that had been trying to stay under the radar, and had not fired a shot.

On the bridge of that ship there was a cloaked figure that exuded an evil aura.

"The Atlantis fleet is suffering heavy loses, most of their ships have been destroyed or disabled." Anubis' First Prime announced. "How ever there is still weapons fire coming from the surface."

"It is of no concern. Rally the bulk of the Wraith hive ships, and focus their fire on Atlantis. With their shields down they will be forced to abandon the city, and then the city will be mine, and you can have their world." Anubis promised, then turned to stare out the window at the battle.

"You're not going to win this."

Anubis spun around to see a man in a robe, obviously he was an ascended being.

"You cannot stop me."Anubis spat.

"I might be bound by the laws of the ascended, fortunately I don't have to drop anymore hints."

Anubis turned to the window to see a massive ship drop out of hyper space.

"The Leviathan!" Anubis said in shock. Then turned to the ascended being. "Why would you risk your ascension to help them?" Anubis demanded.

"For the same reason I piloted an Ancient warship into the sun one year ago."

**Odyssey - Bridge**

"Colonel, most of the hive ships are converging on Atlantis." the helm announced.

"Son of a . . ." Mitchell began, then switched thoughts. "Give me all the power to weapons and shields you can. We're gonna . . . " Mitchell said but someone cut him off mid sentence.

"Sir, I 'm detecting a massive hyper space window opening."

A massive ship emerged from the window. There was a brief yet nerve-racking pause.

"I'm getting a message."

"Put it through." Mitchell requested.

The request was executed.

"The cavalry has arrived!" Colonel Sheppard announced.

"What took you?" Mitchell demanded.

"Oh, you know. We couldn't find a ship that we really liked." Sheppard remarked.

**Leviathan - Bridge**

"Do you think they have any idea what's about to happen to them?" Ronon asked.

"Not a chance." Carter replied.

"Good." Sheppard added, then seemed to focus on something else.

From the Odyssey's vantage point they could see billions of tiny missiles swarm out of the Leviathan, with support from massive amounts of Asgard weapons fire putting Anubis' fleet in a desperate situation, throwing everything they had at Atlantis, and the Leviathan.

In the end, it was all for naught.

Anubis' flagship was the last ship destroyed. Everything else was destroyed or fled into hyper space.

**Atlantis - Stargate Ops**

The day following the harrowing battle above Atlantis, Woolsey was over looking the city from his 'spot' when Rodney found him.

"I have some good news, and some bad news." Rodney began.

Woolsey turned away from the vista.

"What's the bad news." Woolsey began, he wanted to get the bad news out of the way. Maybe the good news would make the bad news not as bad.

"The bad news is we detected a momentary power spike coming from Anubis' ship before it exploded." Rodney started.

Woolsey looked concerned at the revelation.

"What could have caused that?"Woolsey asked.

"It could have just been a power capacitor overloading, or. . . "Rodney paused hoping what he was about to say wasn't the truth.

"He could have escaped, and is likely half way across the galaxy, you know, plotting his revenge." Rodney concluded. "But the good news is if the rest of the fleet comes back . . ."

Woolsey finished Rodney's sentence. "We'll be waiting." Woolsey turned back towards the outer edge of the city. He was bothered by something, miraculously, Rodney noticed.

"What's wrong?"

"Anubis had access to Asgard time dilation field technology." Woolsey prompted.

"Well, as you know several years ago he took out an Asgard ship, and probed the mind of an Asgard. He must have gotten it from the Asgard then." Rodney guessed.

"That's not the problem." Woolsey paused for effect. "What other knowledge did he have?"

Woolsey was pondering over these disturbing thoughts form more than a minute or two before the city was rocked by a large explosion.

A split second later Woolsey was on the radio with Chuck.

"What happened?" Woolsey asked.

"We're still not sure, power's out across the entire East pier." Chuck replied.

There was a few second seconds before power was out throughout the entire city.

"The Z.P.M. room!" McKay said, identifying the possible source for the primary power outage.

McKay and Woolsey took off running.

"Colonel Sheppard, Major Lorne, meet us in the Z.P.M. room with two more teams of Marines." Woolsey anxiously requested.

Arriving near the Z.P.M. room Major Lorne set up a perimeter while Sheppard and Ronon lead the way into the Z.P.M. room to find the Z.P.M. was missing.

"Ok, this could be a problem." Sheppard announced, though it was rather obvious.

Woolsey entered and was briefly briefed by Sheppard.

Something seemed out of place, metaphorically.

Though the city was no longer running on the power from the Z.P.M. they still had the naquadah generators.

"Control Room, the Z.P.M. has gone missing, you should be able to locate it with the city's sensors." Woolsey said.

When there was no response Woolsey tried to contact the control room again.

"It could be a problem with communications." Rodney suggested.

"Maybe. . . But I don't like it." Woolsey commented. "Colonel Sheppard, take Major Lorne's team, and the two teams of Marine's and go to the control room."

"You think someone escaped from the battle and is sabotaging the city?" Sheppard inquired.

"I would rather not take any chances." Woolsey retorted.

**Atlantis Gate Room**

Dr. Keller was beaming down after assisting with medical treatment of the injuries on the Apollo.

Jennifer walked up to the stairs to the control room to deliver a preliminary report.

As she reached the top of the stairs dozens of Wraith storm in stunning all of the armed Marines and swarm around all of the gate technicians, corralling them down in the middle of the gate room floor.

Amelia Banks inconspicuously activated the link on her headset.

"Chuck, just do as they say. There are dozens of Wraith. If they wanted us dead, we'd be dead." Amelia said knowing that everyone in the huge city was monitoring the general channel she was on.

"Don't be so sure, I may very well have you all killed." Anubis said as he floated across the floor towards the people either kneeling or laying stunned on the floor.

Within seconds the Wraith began removing the headsets from the personnel, conscious or not.

**Temporary Command Point**

It had only been a minute or two since Sheppard heard Amelia announce that there were Wraith in Stargate Ops, and had established a temporary location to strike at the Wraith.

"Near as we can figure, there are two dozen Wraith in the control room, we'll need to come in from all angles and cut off their retreat through the Stargate." Sheppard began.

"Colonel Sheppard, I have another idea." Came a maddeningly familiar voice from a man dressed in a khaki brown hooded robe. "Just shoot when you get my signal!"

**Atlantis - Gate room.**

Anubis paced around the room, saying nothing. So Jennifer spoke up.

"We defeated you, how did you survive?" Jennifer demanded in a fainthearted tone.

Anubis was taken aback at her feigned courage.

"I was not aboard my ship when you destroyed it." Anubis bragged. "But soon I will have a new ship, one with enough fire power to enslave to world of the Tau'ri."

"So, why don't you kill us, and get it over with?" Jennifer demanded.

"Because he's waiting for me!"

Everyone turned to see a man standing in the middle of the seated crowd. They watched in awe and shock as the man extended his arms and several dozen bolts of lightning lanced out and struck down all of the Wraith.

The man glanced towards the base of the stairs, Sheppard wasn't there yet.

"What are you doing here? You cannot interfere." Anubis spat.

The man turned away from the stairs when he saw Sheppard and Major Lorne moving into position.

"That's where you're wrong." the man disagreed.

Anubis jerked as though he was hit by a wave of energy, and the cloak and black shield quickly dissipated revealing a man of flesh and blood.

Anubis' eyes flashed they way a Goa'uld's eyes glow briefly.

"What have you done?" Anubis demanded.

The man turned solemn. "We're mortal!"

That was the signal. Sheppard and Major Lorne fired several shots in rapid succession as the seated crowd ducked to avoid any stray bullets.

When the smoke cleared, and Sheppard approached the man lying on the ground, he stood.

"Colonel Sheppard, well done."

"Thanks . . . who are you?" Sheppard asked. Several people approached the fatally wounded Anubis, lying dead on the ground.

"My name is Dr. Vince Riley."

"Do we know you?" Major Lorne asked.

"Actually, yes. You see one year ago I ascended after ramming a ship into the sun, sealing a tear that threatened Atlantis. I became familiar with an ascended being known as Ganos Lal, she and several others decided that Anubis' plan needed to be stopped. I managed to convince enough of the ascended beings to descend Anubis. All it cost me was my ascension. Soon my memories will fade." Vince explained.

"That's all is it?" Sheppard asked.

About this time, Richard Woolsey arrived in the gate room. A glance around the room gave him most of the information he needed. Sheppard filled in the rest.

"This – guy took out the Wraith, Major Lorne and I took down Anubis."

Woolsey looked at the strange man. Then looked at Sheppard. "Take them all to the Infirmary, and have them checked out."

Sheppard and Lorne escorted the four people to the Infimary.

There Sheppard and Woolsey got the explanation they wanted.

"Now with Anubis in the time dilation field building up his fleet, it became clear that the only way to stop him and save Atlantis, I had to convince enough of the Ascended beings to let me step in. I was met with resistance, so I managed to tie my own ascension to that of Anubis."

"When you descend, it forced Anubis down too." Woolsey finished.

"Now that Anubis is dead, I don't think we'll see him again." Sheppard said, then paused, looked over to Jennifer Keller. "He is dead, isn't he?"

"You shot him six times in the chest, three slugs penetrated his heart." Jennifer summarized.

"So that's a Yes?" Sheppard asked.

"That's a yes." Dr. Keller confirmed. Then looked at a corpse lying under a sheet on a nearby bed. "He's finally dead!"

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Thank you for your reviews, thank you for enjoying, thanks for your input. God Bless!


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